JAMM Peak Finder
JAMM: a peak finder for joint analysis of NGS replicates
Publication:
M. Ibrahim, S. Lacadie, U. Ohler (2015). JAMM: a peak finder for joint analysis of NGS replicates. Bioinformatics.
Abstract
We developed JAMM ( J oint A nalysis of NGS replicates via M ixture M odel clustering): a peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is applicable to different types of datasets. We show that JAMM is among the best performing peak finders in terms of site detection accuracy and in terms of accurate determination of enrichment sites widths. In addition, JAMM’s replicate integration improves peak spatial resolution, sorting and peak finding accuracy.
JAMM is a peak finder for NGS datasets that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets.
You can use JAMM to get peaks for DNase-Seq, ChIP-Seq (broad and punctate histone modifications as well as transcription factors), ATAC-seq and many other things
Download
All versions of JAMM and changelog are available on github
Documentation
Main JAMM documentation is available on JAMM's Wiki.
More Information and Tutorials
JAMM's homepage on Github has more information and documentation: https://github.com/mahmoudibrahim/JAMM